Updated p_delete to actually find the location of the library locat…

…ion for each package.

Updated documentation (thinks like adding \code{TRUE})

`Added XML to importFrom and fixed in p_search_any`, `p_help`

Removed unnecessary `cat`s

DESCRIPTION

@@ -4,18 +4,19 @@ Title: Package Management Tool
 Version: 0.2.0
 Date: 2012-06-03
 Authors@R: c(person("Tyler", "Rinker",
-        role = c("aut", "cre", "ctb"),
-        email = "[email protected]"),
+    role = c("aut", "cre", "ctb"),
+    email = "[email protected]"),
     person("Dason", "Kurkiewicz",
-        role = c("aut", "ctb"),
-        email = "[email protected]"))
+    role = c("aut", "ctb"),
+    email = "[email protected]"))
 Author: Tyler Rinker & Dason Kurkiewicz
 Maintainer: Tyler Rinker <[email protected]>
 Depends:
     R (>= 2.13.0)
-Suggests:
-    lattice,
+Imports:
     XML
+Suggests:
+    lattice
 BugReports: https://github.com/trinker/pacman/issues?state=open
 Description: This package is a designed to more conveniently perform tasks
     associated with add on packages.  pacman conveniently wraps library and

NAMESPACE

@@ -41,3 +41,7 @@ export(p_version)
 export(p_vign)
 export(p_vignette)
 export(p_zip)
+importFrom(XML,getNodeSet)
+importFrom(XML,htmlTreeParse)
+importFrom(XML,readHTMLTable)
+importFrom(XML,xmlValue)

R/p_author.R

@@ -12,5 +12,5 @@
 p_author <-
 function(package = "base"){
     x <- as.character(substitute(package))
-    packageDescription(x)$Author
+    packageDescription(x)[["Author"]]
 }

R/p_base.R

@@ -1,11 +1,12 @@
 #' List all the packages in a base install
 #' 
-#' List all the packages in a base install
+#' List all the packages and marks those in a base install
 #' 
-#' @param open logical. If TRUE opens the directory of the base install packages
-#' @param basemarker character string.  The string to append to mark which packages
-#' are part of the default packages.
-#' @note Packages that are installed when R starts are marked with an asterisk(*)
+#' @param open logical. If \code{TRUE} opens the directory of the base install 
+#' packages.
+#' @param basemarker character string.  The string to append to mark which 
+#' packages are part of the default packages.
+#' @note Packages that are installed when R starts are marked with an asterisk(*).
 #' @seealso \code{\link[base]{getOption}}
 #' @keywords base package
 #' @export
@@ -28,7 +29,7 @@ function(open = FALSE,  basemarker = "***"){
     if (open) { 
         p_opendir(basepath)
     }
-    cat('\npackages with an', basemarker, 'are loaded when R starts\n\n')
+    message('\npackages with an', basemarker, 'are loaded when R starts\n\n')
     print(noquote(modified_output))
     invisible(basefiles)
 }

R/p_citation.R

@@ -4,8 +4,11 @@
 #' 
 #' @rdname p_citation
 #' @param package Name of the package you want a citation for
-#' @param copy2clip logical.  If TRUE attempts to copy the output to the 
+#' @param copy2clip logical.  If \code{TRUE} attempts to copy the output to the 
 #' clipboard
+#' @param tex logical.  If \code{TRUE} A only the BibTex version of the citation
+#' is copied to the clipboard.  If \code{FALSE} The standard citation is copied 
+#' to the clipboard.  If \code{NULL} both are copied to the clipboard.
 #' @param \ldots Additional inputs to \code{\link[utils]{citation}}
 #' @seealso \code{\link[utils]{citation}}
 #' @keywords citation cite
@@ -14,15 +17,40 @@
 #' p_citation()
 #' p_cite(pacman)
 #' p_citation(pacman)
-p_citation <- function(package = "r", copy2clip = TRUE, ...) {
+p_citation <- function(package = "r", copy2clip = TRUE, tex = TRUE, ...) {
     x <- as.character(substitute(package))
 
     if(x %in% c("R", "r")){
         # To cite R we need to use package = "base"
         x <- "base"
     }
+
     if(copy2clip){
+        ## Grab citation to optionally manipulate 
+        ## and copy to clipboard
         out <- capture.output(citation(package = x, ...))
+
+        if (!is.null(tex)) {
+
+            loc <- grep("BibTeX entry for LaTeX", out)
+
+            if (isTRUE(tex)) {  
+                ## Grab only the bibtex portion
+                locs <- (1 + loc):length(out)
+            } else {
+
+                ## Remove the `To cite in publications, please use:` 
+                grab <- seq_along(out) != grep("in publications, please use", out)
+                out <- out[grab]
+
+                ## Grab only the standard portion
+                locs <- 1:(loc - 1)
+            }
+
+            out <- out[locs]
+            out <- out[out != ""]
+            out <- paste(substring(out, 3), collapse="\n")
+        }
         writeToClipboard(out)            
     }   
     citation(package = x, ...)

R/p_cran.R

@@ -2,8 +2,8 @@
 #' 
 #' Generate a vector of all available packages.
 #' 
-#' @param menu logical.  If TRUE allows user to select 
-#' the package and return that package name
+#' @param menu logical.  If \code{TRUE} allows user to select the package and 
+#' return that package name.
 #' @seealso \code{\link[utils]{available.packages}}
 #' @keywords CRAN package
 #' @export

R/p_data.R

@@ -2,12 +2,12 @@
 #' 
 #' Generate a script of all data sets contained in package.
 #' 
-#' @param package name of package (default is the base install datasets package)
-#' @param static logical.  If TRUE a static txt docuemnt is returned (e.g. 
-#' \code{data("datasets")}).
+#' @param package name of package (default is the base install datasets package).
+#' @param static logical.  If \code{TRUE} a static text docuemnt is returned 
+#' (e.g. \code{data("datasets")}).
 #' @seealso \code{\link[utils]{data}}
 #' @return Returns the data sets of a package as dataframe 
-#' (\code{static = FALSE}) or as a static txt file (\code{static = TRUE}).
+#' (\code{static = FALSE}) or as a static text file (\code{static = TRUE}).
 #' @keywords data package
 #' @export
 #' @examples

R/p_delete.R

@@ -17,48 +17,62 @@
 #' p_delete(pacman) # You never want to run this
 #' }
 p_delete <-
-function (...) 
-{
+function (...) {
     mf <- match.call(expand.dots = FALSE)
-    x <- as.character(mf[[2]])   
-    lp <- .libPaths()[1]
-    z <- x[!x %in% dir(lp)]
-
-    ## TODO: We definitely need to rewrite
-    ## to better detect where the package actually
-    ## is stored
-    m <- dir(.libPaths()[2])
-    o <- z[z %in% dir(.libPaths()[2])]
-    z <- z[!z %in% dir(.libPaths()[2])]
-    y <- x[x %in% dir(lp)]
-    y2 <- paste0("package:", y)
-    w <- y %in% names(sessionInfo()[["otherPkgs"]])
-    if (any(w)) {
-        u <- y2[w]
-        invisible(lapply(u, function(package) {
+    packs <- as.character(mf[[2]]) 
+    pack_check <- sapply(packs, function(x) system.file(package = x))
+
+    ## Generate list of packages present/absent in a library 
+    absent <- nulls(names(pack_check[pack_check == ""]))
+    base_install <- rownames(installed.packages(priority="base"))
+    bcheck <- basename(pack_check) %in% c(base_install)
+    base <- nulls(basename(pack_check)[bcheck])
+    present <- nulls(pack_check[!bcheck & pack_check != ""])
+
+    ## Unload any package that will be deleted
+    loaded <- basename(present) %in% names(sessionInfo()[["otherPkgs"]])
+    if (any(loaded)) {
+        unloads <- sprintf("package:%s", basename(present)[loaded])
+        invisible(lapply(unloads, function(package) {
             suppressWarnings(detach(package, character.only = TRUE, 
                 force = TRUE, unload = TRUE))
         }))
     }
-    if (length(y) > 0){
-        suppressWarnings(remove.packages(y, lib = lp))
+
+    ## Force delete the files
+    if (length(present) > 0){
+        suppressWarnings(remove.packages(pkgs = basename(present), 
+           lib = dirname(present)))
     }
-    y <- paste(y, collapse = ", ")
-    if (!identical(o, character(0))) {
-        cat(paste0("The following packages are a base ", 
-            "install and will not be deleted:\n"), 
-            paste0("\b", paste(o, collapse = ", ")), "\n\n")
+
+    ## Message about base package not removed
+    if (!is.null(base)) {
+        message("The following packages are a base ", 
+            "install and will not be deleted:\n", 
+            paste(base, collapse = ", "), "\n")
     }
-    if (!identical(z, character(0))) {
-        cat("The following packages not found in library:\n", 
-            paste0("\b", paste(z, collapse = ", ")), "\n\n")
+
+    ## Message about files not found
+    if (!is.null(absent)) {
+        message("The following packages not found in library:\n", 
+            paste(absent, collapse = ", "), "\n")
     }
-    if (length(y) > 0) {
-        cat("The following packages have been deleted:\n", paste0("\b", 
-            paste(y, collapse = ", ")), "\n")
+
+    ## Message about deleted files
+    if (length(present) > 0) {
+        message("The following packages have been deleted:\n",  
+            paste(basename(present), collapse = ", "))
     }
 }
 
+## Helper to check for as.character(0) and turn to NULL
+nulls <- function(x, ret = NULL) {
+    if (identical(x, character(0))){
+        x <- ret
+    }    
+    x
+}
+
 #' @rdname p_delete
 #' @export
 p_del <- p_delete

R/p_exists.R

@@ -3,8 +3,8 @@
 #' Checks CRAN to determine if a package exists
 #' 
 #' @param package name of package
-#' @param cran logical.  If TRUE checks CRAN for the package; 
-#' if FALSE checks the user's local library
+#' @param cran logical.  If \code{TRUE} checks CRAN for the package; 
+#' if \code{FALSE} checks the user's local library.
 #' @keywords exists package
 #' @export
 #' @examples
@@ -14,8 +14,7 @@
 #' p_exists(I_dont_exist)
 #' }
 p_exists <-
-function (package, cran = TRUE) 
-{
+function (package, cran = TRUE) {
     x <- as.character(substitute(package))
     if (cran){
         a <- available.packages()

R/p_functions.R

@@ -4,10 +4,10 @@
 #' 
 #' @rdname p_functions
 #' @param package Name of the package you want the list of functions for.
-#' @param all logical.  If TRUE all of the functions from the package will
-#' be displayed regardless of whether they're exported or not.
-#' @param load logical.  If TRUE loads the package.
-#' @param character.only logical. If TRUE the input is a variable 
+#' @param all logical.  If \code{TRUE} all of the functions from the package 
+#' will be displayed regardless of whether they're exported or not.
+#' @param load logical.  If \code{TRUE} loads the package.
+#' @param character.only logical. If \code{TRUE} the input is a variable 
 #' containing the package name.
 #' @keywords function package
 #' @export
@@ -51,7 +51,8 @@ function (package = "base", all = FALSE, load = FALSE, character.only = FALSE){
 
     ## Should we mark non-exported functions with asterisks or something?
     if(all){
-        packagefunctions <- unclass(lsf.str(envir = asNamespace(package), all = T))
+        packagefunctions <- unclass(lsf.str(envir = asNamespace(package), 
+        	all = TRUE))
         # Removes pesky attributes.
         attributes(packagefunctions) <- NULL
     }else{

R/p_help.R

@@ -2,13 +2,14 @@
 #'
 #' Generate an html, web or pdf of a package's help manual
 #' 
-#' @param package name of package
-#' @param web logical.  If TRUE grabs current help manual from the web
-#' @param pdf logical.  If TRUE uses a LaTeX compiler to generate a pdf
+#' @param package Name of package.
+#' @param web logical.  If \code{TRUE} grabs current help manual from the web.
+#' @param pdf logical.  If \code{TRUE} uses a LaTeX compiler to generate a pdf
 #' @section Warning:
 #' To use the pdf argument you must have a pdf compiler (e.g. MikTex) installed.
 #' @keywords help manual package
 #' @seealso \code{\link[utils]{help}}
+#' @importFrom XML htmlTreeParse getNodeSet xmlValue
 #' @export
 #' @examples
 #' \dontrun{
@@ -24,12 +25,9 @@ function (package = NULL, web = FALSE, pdf = FALSE) {
         x <- "base"
     y <- list.files(.libPaths())
     if (web) {
-        if(!require("XML")){
-            install.packages("XML")
-        } 
-        suppressPackageStartupMessages(p_load("XML"))
+
         url <- "http://stat.ethz.ch/R-manual/R-patched/library/"
-        doc <- XML::htmlTreeParse(url, useInternalNodes = TRUE)
+        doc <- htmlTreeParse(url, useInternalNodes = TRUE)
         content <- getNodeSet(doc, "//pre//text()")
         content <- sapply(content, xmlValue)
         content <- content[10:length(content)]

R/p_interactive.R

@@ -1,8 +1,7 @@
 #' Interactive package exploration
 #' 
-#' Interactively search through packages, looking 
-#' at functions and optionally attaching the package 
-#' and looking at the help page.
+#' Interactively search through packages, looking at functions and optionally 
+#' attaching the package and looking at the help page.
 #' 
 #' @rdname p_interactive
 #' @keywords package
@@ -26,14 +25,14 @@ function() {
             sep = ""), character.only = TRUE)))
     }
     y <- menu(objects(paste("package:", pack, sep = "")))
-    cat("Available Functions\n")
+    message("Available Functions\n")
     fun <- objects(paste("package:", pack, sep = ""))[y]
     z2 <- switch(menu(c(cat("\n\nDo you want to see the help page for", 
         fun, "\b?\n"), "Yes", "No")), TRUE, FALSE)
     if (z2) {
         help((fun))
     } 
-    cat("Thank you for using the p_interactive function!\n\n")
+    message("Thank you for using the p_interactive function!\n\n")
 }
 
 #' @rdname p_interactive

R/p_library.R

@@ -6,8 +6,8 @@
 #' packages are stored).
 #' 
 #' @rdname p_library
-#' @param open logical. If TRUE opens the directory of 
-#' the add on packages library.
+#' @param open logical. If \code{TRUE} opens the directory of the add on 
+#' packages library.
 #' @keywords library package
 #' @export
 #' @examples